Index of Cell Identity (ICI)

Working directory must contain subdirectories,supp_data and src

Working directory should contain root atlas Seurat object, which is available on GEO under record GSE152766:

Root_Atlas.rds (or get it by running through notebook 2)

supp_data/ should contain the files, which are available on Github (github.com/Hsu-Che-Wei/COPILOT):

marker_metadata.csv  
ici_metadata.csv
Protoplasting_DEgene_FC2_list.txt (from Denyer, et al. 2019)
ATH1-121501.na36.annot.csv.bz2 (From Affymetrix)
included_cell_types.csv

supp_data/ should also contain the directory:

published_datasets/

supp_data/published_datasets/ should contain counts data from the RNASeq datasets:

published_datasets/RNASeq_counts.csv

src_ICI/ must contain the file:

ICI_functions.R

1. Load data

2. Build normalized expression data table

3. Compute specification table

4. Filter dataset

5. Re-compute specification tables

6. Compute ICI scores

7. Save ICI output

8. Plot ICI scores on UMAP